Research Article
Investigation of Potential Antibacterial Properties of Some Azo Compounds by Molecular Docking Method
Abstract
In
this study, molecular docking studies were applied to three azo dyes,
2-[(3,5-diamino-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (A),
2-[(3,5-dimethyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (B) and
2-[(5-amino-3-methyl-1H-pyrazol-4-yl)diazenyl]-5-nitrobenzoic acid (C), which
synthesized in our previous studies, to investigate their potential
antibacterial properties. Modelling was performed on SwissDock web server using
EADock DSS algorithm. Docking simulations of ligands (A, B and C) were
performed into the E. coli beta-ketoacyl-acyl
carrier protein synthase III (KAS III) active site to determine the probable
binding conformations and inhibitory effects. Docking results were also
compared with triclosan used as a commercial antibacterial agent and it was
found that compound B had the best antibacterial property.
References
- J. Lee, S. Kim, J. Sim, D. Lee, H. H. Kim, J. S. Hwang, D. G. Lee, Z. Y. Park, and J. I. Kim, “A potent antibacterial activity of new short D-enantiomeric lipopeptide against multi drug resistant bacteria,” Biochim Biophys Acta Biomembr., 1861, 34-42, 2019.
- S. Tahir, T. Mahmood, F. Dastgir, I. Haq, A. Waseem, and U. Rashid, “Design, synthesis and anti-bacterial studies of piperazine derivatives against drug resistant bacteria,” Eur J Med Chem., 166, 224-231, 2019.
- M. Caniçaa, V. Manageiro, H. Abriouel, J. Moran-Giladd, and C.M.A.P. Franzg, “Antibiotic resistance in foodborne bacteria,” Trends Food Sci. Technol., 84, 41-44, 2019.
- I.J. Schalk, “Siderophoreeantibiotic conjugates: exploiting iron uptake to deliver drugs into bacteria,” Clin. Microbiol. Infect., 24, 801-802, 2018.
- F. R. Fields, S. W. Lee, and M. J. McConnell, “Using bacterial genomes and essential genes for the development of new antibiotics,” Biochem. Pharmacol., 134, 74–86, 2017.
- Ç. Karabacak Atay, T. Tilki, and B. Dede, “Design and synthesis of novel ribofuranose nucleoside analogues as antiproliferative agents: A molecular docking and DFT study,” J. Mol. Liq., 269, 315–326, 2018.
- P. Sledz, and A. Caflisch, “Protein structure-based drug design: from docking to molecular Dynamics,” Curr. Opin. Struc. Biol., 48, 93–102, 2018.
- S. Kumar, and S. Kumar, “Chapter 6: Molecular Docking: A Structure-Based Approach for Drug Repurposing,” In Silico Drug Design, 161-189, 2019.
- K. A. Ramsbottoma, D. F. Carrb, A. R. Jonesa, and D. J. Rigdena, “Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions,” Mol. Immunol., 101, 488-499, 2018.
- Ç. Karabacak Atay, M. Gokalp, S. Ozdemir Kart, and T. Tilki, “Mono azo dyes derived from 5-nitroanthranilic acid: Synthesis, absorption properties and DFT calculations,” J. Mol. Struct., 1141, 237-244, 2017.
- A. Grosdidier, V. Zoete, and O. Michielin, “SwissDock, a protein-small molecule docking web service based on EADock DSS,” Nucleic Acids Res., 39, 270-277, 2011.
- Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., (2000). The Protein Data Bank. Nucleic Acids Res., 28(1), 235–242.
- Gaussian 09, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
- E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, “UCSF Chimera--a visualization system for exploratory research and analysis,” J. Comput. Chem., 13, 1605-1612, 2004.
- A.D. Becke, “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys. Rev. A, 38, 3098-3100, 1988.
- C. Lee, W. Yang, and R.G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B, 37, 785-789, 1988.
Moleküler Docking Yöntemi ile Bazı Azo Bileşiklerinin Potansiyel Antibakteriyel Özelliklerinin İncelenmesi
Abstract
Bu
çalışmada, önceki çalışmalarımızda sentezlediğimiz üç azo boyarmaddenin, 2 -
[(3,5-diamino-1H-pirazol-4-il)diazenil]-5-nitrobenzoik asit (A),
2-[(3,5)-dimetil-1H-pirazol-4-il) diazenil]-5-nitrobenzoik asit (B) ve
2-[(5-amino-3-metil-1H-pirazol-4-il) diazenil]-5-nitrobenzoik asit (C),
potansiyel antibakteriyel özelliklerini araştırmak için moleküler doking
çalışmaları yapıldı. Modelleme,
SwissDock web sunucusunda EADock DSS algoritması kullanılarak gerçekleştirildi. Olası
bağlanma konformasyonları ve inhibe edici etkileri belirlemek için E. coli beta-ketoaçil-açil taşıyıcı
protein sentaz III (KAS III) aktif bölgesine ligandların (A, B ve C) bağlanma
simülasyonları yapıldı.
Doking sonuçları ayrıca ticari bir antibakteriyel madde olarak
kullanılan triklosan ile karşılaştırıldı ve B bileşiğinin en iyi antibakteriyel
özelliğe sahip olduğu bulundu.
References
- J. Lee, S. Kim, J. Sim, D. Lee, H. H. Kim, J. S. Hwang, D. G. Lee, Z. Y. Park, and J. I. Kim, “A potent antibacterial activity of new short D-enantiomeric lipopeptide against multi drug resistant bacteria,” Biochim Biophys Acta Biomembr., 1861, 34-42, 2019.
- S. Tahir, T. Mahmood, F. Dastgir, I. Haq, A. Waseem, and U. Rashid, “Design, synthesis and anti-bacterial studies of piperazine derivatives against drug resistant bacteria,” Eur J Med Chem., 166, 224-231, 2019.
- M. Caniçaa, V. Manageiro, H. Abriouel, J. Moran-Giladd, and C.M.A.P. Franzg, “Antibiotic resistance in foodborne bacteria,” Trends Food Sci. Technol., 84, 41-44, 2019.
- I.J. Schalk, “Siderophoreeantibiotic conjugates: exploiting iron uptake to deliver drugs into bacteria,” Clin. Microbiol. Infect., 24, 801-802, 2018.
- F. R. Fields, S. W. Lee, and M. J. McConnell, “Using bacterial genomes and essential genes for the development of new antibiotics,” Biochem. Pharmacol., 134, 74–86, 2017.
- Ç. Karabacak Atay, T. Tilki, and B. Dede, “Design and synthesis of novel ribofuranose nucleoside analogues as antiproliferative agents: A molecular docking and DFT study,” J. Mol. Liq., 269, 315–326, 2018.
- P. Sledz, and A. Caflisch, “Protein structure-based drug design: from docking to molecular Dynamics,” Curr. Opin. Struc. Biol., 48, 93–102, 2018.
- S. Kumar, and S. Kumar, “Chapter 6: Molecular Docking: A Structure-Based Approach for Drug Repurposing,” In Silico Drug Design, 161-189, 2019.
- K. A. Ramsbottoma, D. F. Carrb, A. R. Jonesa, and D. J. Rigdena, “Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions,” Mol. Immunol., 101, 488-499, 2018.
- Ç. Karabacak Atay, M. Gokalp, S. Ozdemir Kart, and T. Tilki, “Mono azo dyes derived from 5-nitroanthranilic acid: Synthesis, absorption properties and DFT calculations,” J. Mol. Struct., 1141, 237-244, 2017.
- A. Grosdidier, V. Zoete, and O. Michielin, “SwissDock, a protein-small molecule docking web service based on EADock DSS,” Nucleic Acids Res., 39, 270-277, 2011.
- Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., (2000). The Protein Data Bank. Nucleic Acids Res., 28(1), 235–242.
- Gaussian 09, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016.
- E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, “UCSF Chimera--a visualization system for exploratory research and analysis,” J. Comput. Chem., 13, 1605-1612, 2004.
- A.D. Becke, “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys. Rev. A, 38, 3098-3100, 1988.
- C. Lee, W. Yang, and R.G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B, 37, 785-789, 1988.
There are 16 citations in total.
Details
| Primary Language | English |
|---|---|
| Subjects | Chemical Engineering |
| Journal Section | Makaleler |
| Authors | |
| Publication Date | May 31, 2019 |
| Published in Issue | Year 2019 Volume: 14 Issue: 1 |
